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A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins

M. Madan Babu,^1,3*, M. Leena Priya,^2, A. Tamil Selvan,² Martin Madera,³ Julian Gough,⁴ L. Aravind,¹ and K. Sankaran^2*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,¹ Centre for Biotechnology, Anna University, Chennai 600025, India,² MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom,³ RIKEN Genomic Sciences Centre, W121 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan⁴

Received 10 May 2005/ Accepted 28 October 2005

Lipid modification of the N-terminal Cys residue (N-acyl-S-diacylglyceryl-Cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. Such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. Hence, being able to identify such proteins is of great value. To this end, we have created a comprehensive database of bacterial lipoproteins, called DOLOP, which contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. The website also features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include the following: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/.

These authors contributed equally.

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